In that case it will be possible to store those settings with .indd file, and when .jsx script runs - it can check if those setting exists (in .indd document params) - if so - script can run without showing dialogue with parameters, as all necessary parameters stored with indesign file
I've stored per document settings like this:
app.activeDocument.insertLabel('myLabel', 'myLabelValue');
and then you can get it back out like this:
var myLabel = app.activeDocument.extractLabel('myLabel');